gnu: rust-md5-0.6: Don't hide package.

[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eed40f6..e2b4f6e 100644 (file)
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; GNU Guix --- Functional package management for GNU

-;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net>

 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com>


@@ -297,7 +297,7 @@ provided by UCSC (mm9, July 2007) and stored in Biostrings objects.")
      `(("r-bsgenome" ,r-bsgenome)
        ("r-bsgenome-mmusculus-ucsc-mm9"
         ,r-bsgenome-mmusculus-ucsc-mm9)))
      `(("r-bsgenome" ,r-bsgenome)
        ("r-bsgenome-mmusculus-ucsc-mm9"
         ,r-bsgenome-mmusculus-ucsc-mm9)))

-    (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
+    (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")

     (synopsis "Full masked genome sequences for Mouse")
     (description
      "This package provides full genome sequences for Mus musculus (Mouse) as
     (synopsis "Full masked genome sequences for Mouse")
     (description
      "This package provides full genome sequences for Mus musculus (Mouse) as


@@ -1053,14 +1053,14 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")
 (define-public r-affycoretools
   (package
     (name "r-affycoretools")

-    (version "1.58.3")
+    (version "1.58.4")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "affycoretools" version))
        (sha256
         (base32

-         "12r9ljkp3xix0xq8d1488c8wb3a4whb805v48ynmv985bs3phc71"))))
+         "1p283ysib04qzaayxmrpsmk5bq0jdq2rlky180jrlskpyg6risfw"))))

     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs
     (properties `((upstream-name . "affycoretools")))
     (build-system r-build-system)
     (propagated-inputs


@@ -1071,6 +1071,7 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
        ("r-dbi" ,r-dbi)
        ("r-edger" ,r-edger)
        ("r-gcrma" ,r-gcrma)
        ("r-dbi" ,r-dbi)
        ("r-edger" ,r-edger)
        ("r-gcrma" ,r-gcrma)

+       ("r-glimma" ,r-glimma)

        ("r-ggplot2" ,r-ggplot2)
        ("r-gostats" ,r-gostats)
        ("r-gplots" ,r-gplots)
        ("r-ggplot2" ,r-ggplot2)
        ("r-gostats" ,r-gostats)
        ("r-gplots" ,r-gplots)


@@ -1165,14 +1166,14 @@ the Human Protein Atlas project.")
 (define-public r-regioner
   (package
     (name "r-regioner")
 (define-public r-regioner
   (package
     (name "r-regioner")

-    (version "1.18.0")
+    (version "1.18.1")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "regioneR" version))
        (sha256
         (base32

-         "0m073hrqp62zpd2blnqm5ka539hcilir05m8av14vdhzhjzp13ya"))))
+         "0if7r6njz3ahm545383z5mzmzw8fdvw80a9lfz160j5pcgpx2dq9"))))

     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs
     (properties `((upstream-name . "regioneR")))
     (build-system r-build-system)
     (propagated-inputs


@@ -1399,7 +1400,7 @@ problems in genomics, brain imaging, astrophysics, and data mining.")
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-systempiper" ,r-systempiper)))
        ("r-s4vectors" ,r-s4vectors)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-systempiper" ,r-systempiper)))

-    (home-page "http://bioconductor.org/packages/DiffBind")
+    (home-page "https://bioconductor.org/packages/DiffBind")

     (synopsis "Differential binding analysis of ChIP-Seq peak data")
     (description
      "This package computes differentially bound sites from multiple
     (synopsis "Differential binding analysis of ChIP-Seq peak data")
     (description
      "This package computes differentially bound sites from multiple


@@ -1428,7 +1429,7 @@ occupancy (overlap) analysis and plotting functions.")
        ("r-rsamtools" ,r-rsamtools)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-rtracklayer" ,r-rtracklayer)))
        ("r-rsamtools" ,r-rsamtools)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-rtracklayer" ,r-rtracklayer)))

-    (home-page "http://bioconductor.org/packages/RIPSeeker")
+    (home-page "https://bioconductor.org/packages/RIPSeeker")

     (synopsis
      "Identifying protein-associated transcripts from RIP-seq experiments")
     (description
     (synopsis
      "Identifying protein-associated transcripts from RIP-seq experiments")
     (description


@@ -1457,7 +1458,7 @@ processing to visualization and annotation.")
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-biobase" ,r-biobase)
        ("r-mass" ,r-mass)))
        ("r-biocgenerics" ,r-biocgenerics)
        ("r-biobase" ,r-biobase)
        ("r-mass" ,r-mass)))

-    (home-page "http://bioconductor.org/packages/multtest")
+    (home-page "https://bioconductor.org/packages/multtest")

     (synopsis "Resampling-based multiple hypothesis testing")
     (description
      "This package can do non-parametric bootstrap and permutation
     (synopsis "Resampling-based multiple hypothesis testing")
     (description
      "This package can do non-parametric bootstrap and permutation


@@ -1568,7 +1569,7 @@ determining dependencies between variables, code improvement suggestions.")
        ("r-seqinr" ,r-seqinr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-venndiagram" ,r-venndiagram)))
        ("r-seqinr" ,r-seqinr)
        ("r-summarizedexperiment" ,r-summarizedexperiment)
        ("r-venndiagram" ,r-venndiagram)))

-    (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
+    (home-page "https://bioconductor.org/packages/ChIPpeakAnno")

     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
     (description
      "The package includes functions to retrieve the sequences around the peak,
     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
     (description
      "The package includes functions to retrieve the sequences around the peak,


@@ -1593,7 +1594,7 @@ enrichedGO (addGeneIDs).")
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-limma" ,r-limma)))

-    (home-page "http://bioconductor.org/packages/marray")
+    (home-page "https://bioconductor.org/packages/marray")

     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
 microarray data.  It also includes functions for data input, diagnostic plots,
     (synopsis "Exploratory analysis for two-color spotted microarray data")
     (description "This package contains class definitions for two-color spotted
 microarray data.  It also includes functions for data input, diagnostic plots,


@@ -1614,7 +1615,7 @@ normalization and quality checking.")
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-marray" ,r-marray)))
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-marray" ,r-marray)))

-   (home-page "http://bioconductor.org/packages/CGHbase")
+   (home-page "https://bioconductor.org/packages/CGHbase")

    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 the @code{arrayCGH} packages.")
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 the @code{arrayCGH} packages.")


@@ -1637,7 +1638,7 @@ the @code{arrayCGH} packages.")
       ("r-impute" ,r-impute)
       ("r-dnacopy" ,r-dnacopy)
       ("r-snowfall" ,r-snowfall)))
       ("r-impute" ,r-impute)
       ("r-dnacopy" ,r-dnacopy)
       ("r-snowfall" ,r-snowfall)))

-   (home-page "http://bioconductor.org/packages/CGHcall")
+   (home-page "https://bioconductor.org/packages/CGHcall")

    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 @code{arrayCGH} packages.")
    (synopsis "Base functions and classes for arrayCGH data analysis")
    (description "This package contains functions and classes that are needed by
 @code{arrayCGH} packages.")


@@ -1666,7 +1667,7 @@ the @code{arrayCGH} packages.")
        ("r-matrixstats" ,r-matrixstats)
        ("r-r-utils" ,r-r-utils)
        ("r-rsamtools" ,r-rsamtools)))
        ("r-matrixstats" ,r-matrixstats)
        ("r-r-utils" ,r-r-utils)
        ("r-rsamtools" ,r-rsamtools)))

-    (home-page "http://bioconductor.org/packages/QDNAseq")
+    (home-page "https://bioconductor.org/packages/QDNAseq")

     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
     (description "The genome is divided into non-overlapping fixed-sized bins,
 number of sequence reads in each counted, adjusted with a simultaneous
     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
     (description "The genome is divided into non-overlapping fixed-sized bins,
 number of sequence reads in each counted, adjusted with a simultaneous


@@ -1999,14 +2000,14 @@ genes or proteins in these datasets.")
 (define-public r-inspect
   (package
     (name "r-inspect")
 (define-public r-inspect
   (package
     (name "r-inspect")

-    (version "1.16.0")
+    (version "1.16.2")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "INSPEcT" version))
        (sha256
         (base32

-         "043066zygf2y2jp6dvfwl56hkzcdvkmymhjx3gh4mhi48l71zqv9"))))
+         "1g8la7k4pnyr2hvk4yjd1bwvjy6nqbbb0fwxrrh2ifgqf4h21x2p"))))

     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs
     (properties `((upstream-name . "INSPEcT")))
     (build-system r-build-system)
     (propagated-inputs


@@ -2015,6 +2016,7 @@ genes or proteins in these datasets.")
        ("r-biocparallel" ,r-biocparallel)
        ("r-deseq2" ,r-deseq2)
        ("r-desolve" ,r-desolve)
        ("r-biocparallel" ,r-biocparallel)
        ("r-deseq2" ,r-deseq2)
        ("r-desolve" ,r-desolve)

+       ("r-gdata" ,r-gdata)

        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)
        ("r-genomeinfodb" ,r-genomeinfodb)
        ("r-genomicalignments" ,r-genomicalignments)
        ("r-genomicfeatures" ,r-genomicfeatures)


@@ -3458,14 +3460,14 @@ All the visualization methods are developed based on ggplot2 graphics.")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")
 (define-public r-clusterprofiler
   (package
     (name "r-clusterprofiler")

-    (version "3.14.0")
+    (version "3.14.3")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "clusterProfiler" version))
        (sha256
         (base32

-         "0mm9iafrsjb8sj27k9mg40ab13vq4rmrzhaajm6g1wdkb2jqikjk"))))
+         "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg"))))

     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)
     (properties
      `((upstream-name . "clusterProfiler")))
     (build-system r-build-system)


@@ -3491,14 +3493,14 @@ profiles (GO and KEGG) of gene and gene clusters.")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")
 (define-public r-mlinterfaces
   (package
     (name "r-mlinterfaces")

-    (version "1.66.0")
+    (version "1.66.2")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MLInterfaces" version))
        (sha256
         (base32

-         "1vnzqd3y3jk1wgxybckzrcgwk0ly7zgcz5ki1ib0bk1jwv6xk5x8"))))
+         "1wc280iw9vllg6f58vsdj895yaqs8w42kl7jk8sgii009gwlaj8d"))))

     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs
     (properties `((upstream-name . "MLInterfaces")))
     (build-system r-build-system)
     (propagated-inputs


@@ -3516,7 +3518,6 @@ profiles (GO and KEGG) of gene and gene clusters.")
        ("r-mlbench" ,r-mlbench)
        ("r-pls" ,r-pls)
        ("r-rcolorbrewer" ,r-rcolorbrewer)
        ("r-mlbench" ,r-mlbench)
        ("r-pls" ,r-pls)
        ("r-rcolorbrewer" ,r-rcolorbrewer)

-       ("r-rda" ,r-rda)

        ("r-rpart" ,r-rpart)
        ("r-sfsmisc" ,r-sfsmisc)
        ("r-shiny" ,r-shiny)
        ("r-rpart" ,r-rpart)
        ("r-sfsmisc" ,r-sfsmisc)
        ("r-shiny" ,r-shiny)


@@ -3792,19 +3793,20 @@ fitting a three-component normal mixture on z-scores.")
 (define-public r-rgadem
   (package
     (name "r-rgadem")
 (define-public r-rgadem
   (package
     (name "r-rgadem")

-    (version "2.34.0")
+    (version "2.34.1")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "rGADEM" version))
        (sha256
         (base32

-         "14ylbrzb9haqwfdd9g813mzhll6gwvqf2r7cmbaxz5lkl0j0nglx"))))
+         "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h"))))

     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)
     (properties `((upstream-name . "rGADEM")))
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biostrings" ,r-biostrings)
        ("r-bsgenome" ,r-bsgenome)

+       ("r-genomicranges" ,r-genomicranges)

        ("r-iranges" ,r-iranges)
        ("r-seqlogo" ,r-seqlogo)))
     (home-page "https://bioconductor.org/packages/rGADEM/")
        ("r-iranges" ,r-iranges)
        ("r-seqlogo" ,r-seqlogo)))
     (home-page "https://bioconductor.org/packages/rGADEM/")


@@ -5162,14 +5164,14 @@ packages.")
 (define-public r-ropls
   (package
     (name "r-ropls")
 (define-public r-ropls
   (package
     (name "r-ropls")

-    (version "1.18.0")
+    (version "1.18.6")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ropls" version))
        (sha256
         (base32

-         "05w1zrq92w3jfwq5sdyj27m5qjg4zv7acywia8vd6y5fbgcnyzlp"))))
+         "1sm2fmygrra9gdcs90lmk5y1ag6arga6159kggx4ij8bkhyc66vb"))))

     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)
     (build-system r-build-system)
     (propagated-inputs
      `(("r-biobase" ,r-biobase)


@@ -5584,14 +5586,14 @@ for other R packages to compile and link against.")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")
 (define-public r-flowworkspace
   (package
     (name "r-flowworkspace")

-    (version "3.34.0")
+    (version "3.34.1")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "flowWorkspace" version))
        (sha256
         (base32

-         "0hvbkxyylsygra31l1lxyvbsr5hc50lqy1y7gwrfgrfil4a2m762"))))
+         "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn"))))

     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs
     (properties `((upstream-name . "flowWorkspace")))
     (build-system r-build-system)
     (propagated-inputs


@@ -6449,14 +6451,14 @@ arrays based on fast wavelet-based functional models.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")

-    (version "1.16.0")
+    (version "1.16.1")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32

-         "1ygx7f2sp4b7ilgspm6vqcbjxs7br9s6g3gwcdb978kx03ymp4i8"))))
+         "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g"))))

     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)
     (properties
      `((upstream-name . "variancePartition")))
     (build-system r-build-system)


@@ -7175,14 +7177,14 @@ access.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")

-    (version "1.12.0")
+    (version "1.12.1")

     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32

-         "0hqg0b0hd5msnb4jcn1nbfyy1n1llfkipy2ivwncivkmbdn8psp4"))))
+         "0xpi5qpffg9pn8szkvicpc43a0r534wngyqwvsip8w66zi8c9kpc"))))

     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)
     (properties
      `((upstream-name . "MultiAssayExperiment")))
     (build-system r-build-system)